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对石榴(Punica granatum)转录组数据进行从头组装,预测完整CDS序列的密码子使用偏向性;将石榴转录谱与其他8种蔷薇分支物种基因组编码序列进行同义密码子相对使用度(RSCU)比较,并对石榴WRKY和MYB家族基因进行亚家族进化分析和RSCU比较。结果表明:(1)石榴转录组主要受自然选择压影响。密码子偏向性极强的基因多为细胞相关功能基因;没有密码子使用偏向性的基因多与维持生命活动本质相关。(2)基因差异高表达影响RSCU,CpG二核苷酸富集影响密码子适应性。(3)物种间亲缘关系越近,RSCU值越相似。对蔷薇分支物种密码子进行RSCU比较,石榴与巨桉(Eucalyptus grandis)偏向性基本一致。(4)亚家族功能分化影响密码子偏向性。石榴WRKY亚家族1、4和13在翻译精氨酸、亮氨酸时分别偏向使用AGG、CUC,这与其不断进化的抗逆功能相关。石榴MYB亚家族8在翻译苏氨酸时偏向选择ACA,这与其扩张中的木质化功能相关。
The codon usage bias of the complete CDS sequence was predicted by the de novo assembly of the transcriptome data of Punica granatum. The relative usage of synonymous codons (RSCU) was compared with that of the other 8 species of rose branching genomic sequences , And the subfamily evolution analysis and RSCU of pomegranate WRKY and MYB family genes were compared. The results showed that: (1) pomegranate transcriptome was mainly influenced by natural selection pressure. Mostly codon-biased genes are mostly cell-associated functional genes. There are many genes that have no codon usage bias and are essentially related to life-sustaining activities. (2) The high expression of gene difference affected RSCU, CpG dinucleotide enrichment affected the codon adaptability. (3) The closer the genetic relationship among species, the more similar RSCU values. RSCU comparisons of rose branching species codons showed that pomegranate and Eucalyptus grandis tended to be more or less the same. (4) Subfamily function differentiation affects codon bias. Pomegranate WRKY subfamilies 1, 4 and 13, respectively, favor the use of AGG and CUC when translating arginine and leucine, which is associated with its evolving anti-retrogradation function. Pomegranate MYB subfamily 8 favors the selection of ACA when translating threonine, which is related to its lignification function.